5VBS

Structural basis for a six letter alphabet including GATCKX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.749 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure and Biophysics for a Six Letter DNA Alphabet that Includes Imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione (X) and 2,4-Diaminopyrimidine (K).

Singh, I.Kim, M.J.Molt, R.W.Hoshika, S.Benner, S.A.Georgiadis, M.M.

(2017) ACS Synth Biol 6: 2118-2129

  • DOI: 10.1021/acssynbio.7b00150

  • PubMed Abstract: 
  • A goal of synthetic biology is to develop new nucleobases that retain the desirable properties of natural nucleobases at the same time as expanding the genetic alphabet. The nonstandard Watson-Crick pair between imidazo[1,2-a]-1,3,5-triazine-2(8H)-4( ...

    A goal of synthetic biology is to develop new nucleobases that retain the desirable properties of natural nucleobases at the same time as expanding the genetic alphabet. The nonstandard Watson-Crick pair between imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione (X) and 2,4-diaminopyrimidine (K) does exactly this, pairing via complementary arrangements of hydrogen bonding in these two nucleobases, which do not complement any natural nucleobase. Here, we report the crystal structure of a duplex DNA oligonucleotide in B-form including two consecutive X:K pairs in GATCXK DNA determined as a host-guest complex at 1.75 Å resolution. X:K pairs have significant propeller twist angles, similar to those observed for A:T pairs, and a calculated hydrogen bonding pairing energy that is weaker than that of A:T. Thus, although inclusion of X:K pairs results in a duplex DNA structure that is globally similar to that of an analogous G:C structure, the X:K pairs locally and energetically more closely resemble A:T pairs.


    Organizational Affiliation

    Department of Biochemistry & Molecular Biology, Indiana University School of Medicine , Indianapolis, Indiana 46202, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
reverse transcriptase catalytic fragment
A
259Moloney murine leukemia virusMutation(s): 0 
Gene Names: gag-pol
Find proteins for P03355 (Moloney murine leukemia virus)
Go to UniProtKB:  P03355
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*TP*AP*TP*(DX)P*(DX)P*T)-3')B8Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*(93D)P*(93D)P*AP*TP*AP*AP*G)-3')G8Escherichia coli
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
DX
Query on DX
B
DNA linkingC10 H13 N4 O8 P

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93D
Query on 93D
G
DNA linkingC9 H15 N4 O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.749 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 54.999α = 90.00
b = 145.643β = 90.00
c = 46.876γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
MOLREPphasing
HKLdata reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
MOLREPphasing
SCALEPACKdata scaling
HKLdata scaling
PHENIXrefinement
HKL-3000data scaling
DENZOdata reduction
HKL-3000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-07
    Type: Initial release